Keeping an Eye on COVID Clusters With Rapid Sequencing

Contact tracing is a powerful tool used by public health authorities to help slow the spread of infectious diseases such as COVID-19. Those in close contact with infected individuals can swiftly be informed, tested, and advised to self-isolate, thus lowering the risk of the COVID-19 virus spreading further.

Not every case cluster is so easy to track, however. Scientists have found a way of mapping case networks more efficiently, by leveraging one of the virus’s hallmark flaws. 

“Every time the SARS-CoV-2 virus passes from person to person, it may make copying errors that change a couple of its 30,000 genetic letters”, explains Rowena Bull, a researcher from Australia’s University of New South Wales.

“By identifying this genetic variation, we can establish how different cases of coronavirus are linked – to know where a case was potentially picked up from and who they may have given it to.” 

Bull and colleagues have spearheaded the development of a superior method of contact tracing by employing next-generation genome sequencing technologies. This method provides quick answers as to how COVID cases are linked, enabling improved pandemic-control initiatives.

These guidelines, published in Nature Communications, take advantage of nanopore sequencing. Here, subtle changes in an electric current as DNA or RNA traverses a nano-scale hole in a protein called a nanopore are measured. The signals read by this passage of nucleic acids through the nanopore are then decoded and translated into a sequence. 

One of the main benefits of this platform is its speed. Using this technology, developed by Oxford Nanopore Technologies, the entire 30 kilobase-long SARS-CoV-2 genome can be sequenced in just under four hours.

The new-and-improved form of viral tracking can help trace the origins of variants (such as the highly-contagious UK variant) and bridge the gaps left by traditional epidemiological investigations. It can also be useful in identifying so-called COVID “super-spreaders” in the community. 

Among the concerns around using this relatively new technology for COVID-tracking applications was whether or not it was accurate enough. In their publication, Bull and colleagues demonstrate this not to be the case, detecting variants with >99% sensitivity and >99% precision in a cohort of 157 COVID-positive patient samples.

“Nanopore devices are cheaper, faster, portable and don’t require the lab infrastructure needed by current standard pathogen genomics tools,” said senior author of the study, Ira Deveson, Head of the Genomic Technologies Group. 

“We hope our validation of this protocol will help other public health teams around the world adopt this technology.”

Sources: UNSW Sydney, Nature Communications.